Syrian Loa'l Mohammad Haj Bakr al-Saqa was jailed for masterminding the bombings, which killed more than 50 people and targeted two synagogues, a British consulate, and a London-based bank.
Forty-one other defendants were given various prison terms of up to 18 years, and a further 26 were acquitted.
Defendant lawyer Mehmet Sami Selcuk said the defense would appeal.
"Forty-eight of 72 of suspects have been sentenced," Selcuk said. "This is not the verdict that we are expecting. We will go to appeal court."
The process was Turkey's highest-profile trial since the 1999 conviction of Kurdish guerrilla leader Abdullah Ocalan.
Al-Saqa, a bomb-making expert, was convicted of having masterminded and secured financing for the Istanbul bombings. He was an alleged associate of the late Al-Qaeda leader in Iraq, Abu Mus'ab al-Zarqawi, and was believed to be the top figure in Osama bin Laden's Al-Qaeda network in Turkey.
He was arrested in the southern port city of Antalya in 2005, after explosives accidentally went off in a building he was using as a safe house. Turkish authorities say al-Saqa planned to blow up Israeli cruise ships in the Mediterranean.
Along with al-Saqa, the court also sentenced Harun Ilhan -- who admitted to plotting the bombings and being a member of Al-Qaeda -- to a life sentence, along with Fevzi Yitiz, Yusuf Polat, Baki Yigit, Osman Eken, and Adnan Ersoz -- who were convicted of helping to build the truck bombs.
The court convicted the seven of "attempting to change the [secular] constitutional regime with force," causing deaths and wounding 647 people, and "planning the bombings and providing resources."
Several others were convicted to prison terms.
Seyit Ertul was accused of leading an Al-Qaeda cell in the Turkish town of Konya and was sentenced to 18 years in prison. Hamid Obysi was sentenced to 12 1/2 years for membership of Al-Qaeda, bomb making, and producing false identification cards.
Twenty-nine people received six-year sentences, and 10 more were sentenced to at least three years for helping the bombers.
British Foreign Secretary Margaret Beckett said in a statement that Britain welcomed the verdict.